Open data and open access - A biomedical data- and text-mining perspective

What went wrong with publishing in COVID19. Naomi Hammond walks us through the good, the bad and the ugly aspects of COVID19 publications. The ability for researchers to rapidly design and conduct trials in the midst of a pandemic was valuable. With that however, came an 'infodemic' where consumers struggled to keep up with the abundance of information. In April 2020, there were 6,000 articles published in one month. This caused concerns regarding the quality of publications, the increase in opinion articles and the number of articles which were retracted over the course of Covid. Tune in to a fascinating talk about what went wrong with publishing in COVID19.

Science

Jensen et al., Nature Reviews Genetics, 2012

Jensen et al., Nature Communications, 2014

Eriksson et al., Drug Safety, 2014
Drug introduction Drug discontinuation
Adverse eventNegative modifier Indication Pre-existing
condition
Adverse drug reaction Possible
adverse drug reaction
Adverse event
ADR of
additional drug
Identification start

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At QPS Netherlands (QPS-NL), we have expanded our early stage clinical research capabilities in 2012 to include respiratory clinical trials. To this end, QPS-NL is collaborating with Dr. Zuzana Diamant, research pulmonologist and clinical pharmacologist. Professor Diamant has over 20 years of experience in clinical respiratory trials, with a focus on phases 0, I and II proof-of-concept studies in respiratory allergy, asthma and COPD. Zuzana Diamant is Guest Professor at Skane University, Lund, Sweden; collaborating scientist at University Medical Centre Groningen, Dept. of General Practice; and a member of several international scientific networks including the ATS/ERS taskforce for bronchoprovocation testing (allergen challenge) and two editorial boards. Together with our dedicated research physician and epidemiologist Dr. Tjeert Mensinga, our well-trained research team, and onsite laboratory biomarker facilities, this collaboration now enables us to perform consultancy services. These include study design, study set up and the conduct of respiratory POC-studies combining clinical disease models (e.g. inhaled and nasal allergen and LPS challenges) with non-invasive airway samplings (e.g. nasal lavage, nasal brushings, sputum analysis, exhaled airway analysis) to test targeted therapies.

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In this work, we assess the potential detectability of solar panels made of silicon on an Earth-like exoplanet as a potential technosignature. Silicon-based photovoltaic cells have high reflectance in the UV-VIS and in the near-IR, within the wavelength range of a space-based flagship mission concept like the Habitable Worlds Observatory (HWO). Assuming that only solar energy is used to provide the 2022 human energy needs with a land cover of ∼ 2.4%, and projecting the future energy demand assuming various growth-rate scenarios, we assess the detectability with an 8 m HWO-like telescope. Assuming the most favorable viewing orientation, and focusing on the strong absorption edge in the ultraviolet-to-visible (0.34 − 0.52 µm), we find that several 100s of hours of observation time is needed to reach a SNR of 5 for an Earth-like planet around a Sun-like star at 10pc, even with a solar panel coverage of ∼ 23% land coverage of a future Earth. We discuss the necessity of concepts like Kardeshev Type I/II civilizations and Dyson spheres, which would aim to harness vast amounts of energy. Even with much larger populations than today, the total energy use of human civilization would be orders of magnitude below the threshold for causing direct thermal heating or reaching the scale of a Kardashev Type I civilization. Any extraterrrestrial civilization that likewise achieves sustainable population levels may also find a limit on its need to expand, which suggests that a galaxy-spanning civilization as imagined in the Fermi paradox may not exist.

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Within the uncertainties of involved astronomical and biological parameters, the Drake Equation typically predicts that there should be many exoplanets in our galaxy hosting active, communicative civilizations (ACCs). These optimistic calculations are however not supported by evidence, which is often referred to as the Fermi Paradox. Here, we elaborate on this long-standing enigma by showing the importance of planetary tectonic style for biological evolution. We summarize growing evidence that a prolonged transition from Mesoproterozoic active single lid tectonics (1.6 to 1.0 Ga) to modern plate tectonics occurred in the Neoproterozoic Era (1.0 to 0.541 Ga), which dramatically accelerated emergence and evolution of complex species. We further suggest that both continents and oceans are required for ACCs because early evolution of simple life must happen in water but late evolution of advanced life capable of creating technology must happen on land. We resolve the Fermi Paradox (1) by adding two additional terms to the Drake Equation: foc (the fraction of habitable exoplanets with significant continents and oceans) and fpt (the fraction of habitable exoplanets with significant continents and oceans that have had plate tectonics operating for at least 0.5 Ga); and (2) by demonstrating that the product of foc and fpt is very small (< 0.00003–0.002). We propose that the lack of evidence for ACCs reflects the scarcity of long-lived plate tectonics and/or continents and oceans on exoplanets with primitive life.

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The Bay of Bengal exhibits a diverse and complex topography on its seafloor, characterized by deep trenches, abyssal plains, submarine canyons, seamounts, and volcanic ridges. The topography is influenced by tectonic processes, sediment accumulation from the Himalayas, and river transport. The sediment distribution patterns in the Bay of Bengal are influenced by various factors, including river inputs, ocean currents, and seafloor topography.

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Mitosis...............................pptx

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Recent observations of galaxy clusters and groups with misalignments between their central AGN jets and X-ray cavities, or with multiple misaligned cavities, have raised concerns about the jet – bubble connection in cooling cores, and the processes responsible for jet realignment. To investigate the frequency and causes of such misalignments, we construct a sample of 16 cool core galaxy clusters and groups. Using VLBA radio data we measure the parsec-scale position angle of the jets, and compare it with the position angle of the X-ray cavities detected in Chandra data. Using the overall sample and selected subsets, we consistently find that there is a 30% – 38% chance to find a misalignment larger than ∆Ψ = 45◦ when observing a cluster/group with a detected jet and at least one cavity. We determine that projection may account for an apparently large ∆Ψ only in a fraction of objects (∼35%), and given that gas dynamical disturbances (as sloshing) are found in both aligned and misaligned systems, we exclude environmental perturbation as the main driver of cavity – jet misalignment. Moreover, we find that large misalignments (up to ∼ 90◦ ) are favored over smaller ones (45◦ ≤ ∆Ψ ≤ 70◦ ), and that the change in jet direction can occur on timescales between one and a few tens of Myr. We conclude that misalignments are more likely related to actual reorientation of the jet axis, and we discuss several engine-based mechanisms that may cause these dramatic changes.

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Cyanobacteria (also known as blue-green algae) are ubiquitous photosynthetic microorganisms found in diverse habitats such as fresh water, marine water, moist rocks, etc. The photosynthetic mode of nutrition makes them significant global oxygen producers along with nitrogen-fixing ability of heterocyst and carbon sequestration. Some cyanobacterial species have the ability to perform a dual mode of nutritional procurement. This unique capability of cyanobacteria to utilize both organic (heterotrophic) and inorganic (autotrophic) carbon sources for energy production and growth is termed as mixotrophy which impart nutritional flexibility and competitive ability to them. Cyanobacterial mixotrophy provides the promising avenues in biotechnological applications such as wastewater treatment, bioremediation, pharmaceuticals, food supplements, biofertilizer, coloring agents, synthesis of bioactive compounds and as an agent for eco-friendly bio-fuels generation, etc Mixotrophically grown cyanobacteria, demonstrate significant potential for efficient and economical applications beyond their conventional agricultural application, thereby offering a versatile and impactful resource for future technological and environmental challenges.

mixotrophy in cyanobacteria: a dual nutritional strategy

MansiBishnoi1

The magnetic dynamo cycle of the Sun features a distinct pattern: a propagating region of sunspot emergence appears around 30° latitude and vanishes near the equator every 11 years (ref. 1). Moreover, longitudinal flows called torsional oscillations closely shadow sunspot migration, undoubtedly sharing a common cause2. Contrary to theories suggesting deep origins of these phenomena, helioseismology pinpoints low-latitude torsional oscillations to the outer 5–10% of the Sun, the near-surface shear layer3,4. Within this zone, inwardly increasing differential rotation coupled with a poloidal magnetic field strongly implicates the magneto-rotational instability5,6, prominent in accretion-disk theory and observed in laboratory experiments7. Together, these two facts prompt the general question: whether the solar dynamo is possibly a near-surface instability. Here we report strong affirmative evidence in stark contrast to traditional models8 focusing on the deeper tachocline. Simple analytic estimates show that the near-surface magneto-rotational instability better explains the spatiotemporal scales of the torsional oscillations and inferred subsurface magnetic field amplitudes9. State-of-the-art numerical simulations corroborate these estimates and reproduce hemispherical magnetic current helicity laws10. The dynamo resulting from a well-understood near-surface phenomenon improves prospects for accurate predictions of full magnetic cycles and space weather, affecting the electromagnetic infrastructure of Earth.

The solar dynamo begins near the surface

PESTS OF SUGARCANE - BORERS BORERS 1. Early shoot borer, Chilo infuscatellus, Crambidae, Lepidoptera Symptom of damage: Deadheart in 1-3 month old crop, which can be easily pulled out, rotten portion of the straw coloured dead-heart emits an offensive odour. A number of bore holes at the base of the shoot just above the ground level. Nature of damage: Caterpillar bores into the central shoot and feeds on the internal tissue. This cause interference in the translocation of plant sap and damage the sugar storing tissues. Egg: Flat-scale like eggs are laid in 3-5 rows on the lower surface of leaves in masses of 4-100. The masses are slightly overlapping like tiles. Larva: Larva is dirty white with five dark violet longitudinal stripes and dark brown head. Pupa: Pupation takes place within the tunnel. Caterpillar before pupating makes a large exit hole in the stem and blocks the opening with silken discs. Adult: Pale greyish brown moth with black dots near the costal margin of the forewings and with white hindwings. 2. Internode borer, Chilo sacchariphagus indicus, Crambidae, Lepidoptera Symptom of damage: Internodes constricted and shortened, with a number of boreholes and fresh excreta in the nodal region. Affected tissues reddened. Nature of damage: Caterpillars attack sugarcane plants after 3 months of planting. They bore into the canes near the nodes; entry holes are plugged with excreta. Entry is generally confined to the first five internodes. Egg: Scale-like white eggs are laid by female moths in batches of 9-11, near the midribs, on leaf sheaths or on stem. Larva: White larva with four violet longitudinal stripes and light brown head. Pupa: Pupation takes place in semi-dried leaf sheath. Adult: Pale brown with white hind wings. 3. Top borer, Scirpophaga excerptalis, Pyralidae, Lepidoptera Symptom of damage: Deadheart in grownup canes, which cannot be easily pulled; deadheart reddish brown in colour; parallel row of shot holes in the emerging leaves and red tunnels in the midribs of leaves; bunchy tip due to the growth of side shoots. Nature of damage: Caterpillars are mainly found in the apical portion of the canes, boring through the growing point and down the upper joints until it reaches the sappy portion of the stem, there it feeds on the tissues and destroys the cane. They also bore into the unfolded leaves preferably into the midrib, mining its way to the base. Egg: Eggs are laid on the lower surface of top leaves in clusters particularly near midribs. The clusters are covered with buff coloured hairs. Larva :Smooth, white or cream coloured with a red coloured mid-dorsal line and yellow head. Pupa: Pupation takes place within the larval tunnel in a chamber with an exit hole constructed by the caterpillar. Adult: White coloured moth (with a buff coloured anal tuft in the abdominal tip of female).

Pests of sugarcane_Binomics_IPM_Dr.UPR.pdf

PirithiRaju

METHODS OF TRANSCRIPTOME ANALYSIS....pptx

Hadean zircons provide a potential record of Earth's earliest subduction 4.3 billion years ago. Itremains enigmatic how subduction could be initiated so soon after the presumably Moon‐forming giant impact(MGI). Earlier studies found an increase in Earth's core‐mantle boundary (CMB) temperature due to theaccumulation of the impactor's core, and our recent work shows Earth's lower mantle remains largely solid, withsome of the impactor's mantle potentially surviving as the large low‐shear velocity provinces (LLSVPs). Here,we show that a hot post‐impact CMB drives the initiation of strong mantle plumes that can induce subductioninitiation ∼200 Myr after the MGI. 2D and 3D thermomechanical computations show that a high CMBtemperature is the primary factor triggering early subduction, with enrichment of heat‐producing elements inLLSVPs as another potential factor. The models link the earliest subduction to the MGI with implications forunderstanding the diverse tectonic regimes of rocky planets.

A Giant Impact Origin for the First Subduction on Earth